2011 TRIENNIAL REPORT ON THE CALIFORNIA DEPARTMENT OF FISH AND GAME’S MARINE INVASIVE SPECIES PROGRAM Submitted to the CALIFORNIA STATE LEGISLATURE as required by the Coastal Ecosystems Protection Act of 2006 Prepared and submitted by the California Department of Fish and Game, Office of Spill Prevention and Response Marine Invasive Species Program December 2011 Program Manager Stephen Foss EXECUTIVE SUMMARY California’s Marine Invasive Species Act of 2003 extended the Ballast Water Management Act of 1999, to address the threat of non-native aquatic species (NAS) introductions. Under this Act, the California Department of Fish and Game (DFG) is required to conduct a study of California coastal waters for new NAS that could have been transported in ballast or through hull fouling and to assess the effectiveness of the Marine Invasive Species Program (MISP) in controlling NAS introductions from ship-related vectors. This report fulfills the reporting mandate set forth in Public Resources Code Section 71211 and summarizes the activities and results of DFG’s MISP from July 2008 through June 2011. A field survey of San Francisco Bay was conducted during 2010, as part of a long-term monitoring effort in ports, harbors, estuaries, and the outer coast. From the samples collected, 497 species were identified, of which 98 (20% of all species identified) were classified as introduced, 92 were classified as cryptogenic, and 307 were classified as native to California. The survey revealed 3 NAS that are apparent new records for San Francisco Bay that likely spread from other locations in California, possibly by ballast water or hull fouling. Beginning in 2009, the MISP, in partnership with the Smithsonian Environmental Research Center (SERC) and the Genomics Lab at Moss Landing Marine Laboratories (MLML), initiated a pilot non-native species detection program in San Francisco Bay. The three-year program combines traditional morphological identification with a “next-generation” sequencing process to analyze the DNA extracted en masse from unsorted, complex, whole-community samples collected from artificial settling plates, hard-substrate quadrats, and plankton tows. If effective, this approach would allow monitoring to move forward from traditional, morphologically-based taxonomy to streamlined, community-level monitoring utilizing state-of-the-art molecular genetic tools. DFG staff collaborated with SERC on an analysis of NAS invasion history and vectors in California. Results of the analysis indicate that California, especially San Francisco Bay, plays a pivotal role in marine invasion dynamics for western North America, providing an entry point from which many species spread. Of the 290 NAS (excluding fish and vascular plants) with established populations in western North America, 81% were first recorded in California. Of the 257 NAS established in California, 61% were first recorded in San Francisco Bay and 57% are known from multiple estuaries, suggesting secondary spread. The future direction of the MISP includes changes to the sampling program. MISP will improve sample design by including stratified random sampling and increased replication, with the aim of explicitly measuring and statistically testing for temporal, spatial, taxonomic, and vector differences in NAS diversity (species richness). This statistically robust sampling approach will enable us to test key questions about NAS and understand invasion dynamics in California. ii CONTENTS Executive Summary.............................................................................................. ii Tables ................................................................................................................... v Figures................................................................................................................. vi Definitions ............................................................................................................vii Acronyms............................................................................................................. ix 1.0 Introduction ....................................................................................................1 2.0 Study Plan and Field Surveys........................................................................4 3.0 Special Studies ............................................................................................16 4.0 Database and Quality Assurance.................................................................29 5.0 Summary of NAS Occurrence in California..................................................32 6.0 Future Direction ...........................................................................................41 Literature Cited ...................................................................................................43 Appendix A - A Rationale for Incorporating Molecular-Based Taxonomy in California’s Non-Native Marine and Estuarine Species Detection and Monitoring Program Appendix B - Table: Counts of non-native species sampled per station in San Francisco Bay in 2010 iii TABLES 1. DFG field surveys per year.........................................................................4 2. Habitats sampled at San Francisco Bay sites in 2010 ...............................9 3. Numbers of samples per habitat and sub-region of San Francisco Bay...10 4. Number of taxa and percent introduced species (excluding unresolved taxa) sampled at San Francisco Bay sites ...............................................13 5. Number of NAS, Samples, and NAS per Sample in Sub-bays of San Francisco Bay ..........................................................................................14 6. Number of species by introduction status and % of introduced per habitat in San Francisco Bay ...............................................................................14 7. Morphotaxa identities resolved through matches with GenBank records .....................................................................................................23 8. CANOD taxa designated or undesignated as introduced.........................33 9. Introduced taxa added to CANOD............................................................35 10. Taxonomic changes that occurred among CANOD introduced taxa ........38 iv FIGURES 1. Sampling sites for 2010 San Francisco Bay field survey in sub-regions San Pablo Bay and Suisun Bay. ................................................................6 2. Sampling sites for 2010 San Francisco Bay field survey in sub-region Central San Francisco Bay ........................................................................7 3. Sampling sites for 2010 San Francisco Bay field survey in sub-region South San Francisco Bay...........................................................................8 4. Number of taxa sampled per introduction status classification in the 2010 San Francisco Bay Survey.......................................................................11 5. Percentage of total taxa within each classification for each habitat type sampled in San Francisco Bay, 2010. .....................................................15 6. Settling plate sampling sites for SERC/MLML Settling Plate/Molecular Detection Study........................................................................................18 7. Number of non-native species by geographic region for western North America....................................................................................................25 8. Locations of first records for NAS in California.........................................26 9. Vectors for established NAS in California ................................................27 10. Main menu of CANOD’s public interface..................................................29 11. Native regions of California introduced species .......................................39 12. The number of newly reported NAS by 25-year intervals for California and western North America.............................................................................40 Acknowledgments Sharon Shiba and Karen Bigham contributed to this report through writing, analysis, and data management. Thanks to Jon Geller and Greg Ruiz for reviewing portions of this report. Randy Imai and Mike Sowby made helpful comments on earlier versions of the report. v DEFINITIONS OF TERMS USED IN THIS REPORT Ballast water: Water taken up or released by a ship to stabilize it, or to raise/lower it in the water column. Benthic: Pertaining to the organisms that live on or in the sea bottom. Biodiversity: Number and variety of living organisms; includes genetic diversity, species diversity and ecological diversity. For the purposes of this document, refers to biodiversity of native organisms. Cosmoname: A scientific name used for the same, or similar-looking, taxon around the world. Cryptic: Of or pertaining to two or more species that are morphologically similar but differ genotypically. Cryptogenic: Taxa that are neither demonstrably native nor introduced (Cohen and Carlton 1995, Carlton 1996) because their native range or region is unknown. Epifaunal: Of or describing organisms that live on the ocean floor or other submerged substrates such as sea anemones and barnacles. Exotic Species: Synonym for introduced or non-native species. Fouling: The accumulation and deposition of living organisms and certain non- living material on hard surfaces, most often in an aquatic environment. Genotype: The genetic makeup of an organism. Infaunal: